Citation and License

Genome Biology 2010, 11:R113
doi:10.1186/gb-2010-11-11-r113

Published: 24 November 2010

Abstract

Background

Genetic studies of populations from the Indian subcontinent are of great interest
because of India's large population size, complex demographic history, and unique
social structure. Despite recent large-scale efforts in discovering human genetic
variation, India's vast reservoir of genetic diversity remains largely unexplored.

Results

To analyze an unbiased sample of genetic diversity in India and to investigate human
migration history in Eurasia, we resequenced one 100-kb ENCODE region in 92 samples
collected from three castes and one tribal group from the state of Andhra Pradesh
in south India. Analyses of the four Indian populations, along with eight HapMap populations
(692 samples), showed that 30% of all SNPs in the south Indian populations are not
seen in HapMap populations. Several Indian populations, such as the Yadava, Mala/Madiga,
and Irula, have nucleotide diversity levels as high as those of HapMap African populations.
Using unbiased allele-frequency spectra, we investigated the expansion of human populations
into Eurasia. The divergence time estimates among the major population groups suggest
that Eurasian populations in this study diverged from Africans during the same time
frame (approximately 90 to 110 thousand years ago). The divergence among different
Eurasian populations occurred more than 40,000 years after their divergence with Africans.

Conclusions

Our results show that Indian populations harbor large amounts of genetic variation
that have not been surveyed adequately by public SNP discovery efforts. Our data also
support a delayed expansion hypothesis in which an ancestral Eurasian founding population
remained isolated long after the out-of-Africa diaspora, before expanding throughout
Eurasia.